Learners with special needs education are of diverse categories. Among them are the Physically Handicapped (PH) .These learners may lag in education if there are no environmental and instructional adaptations to enable them compete on equal footing with their non-disable peers. Among the learners with PH are those with postures that make them strain when they stay in a given position for long like the case of paraplegia. This affects their learning ability by reducing their degree of concentration in studies. The study focused on those with no or weaker upper limps due to the disability. Mathematics has been the worst performed subject among the PH learners in the Kenya Certificate of Secondary Education (KCSE) as indicated in the results of the years 2007 to 2013.The means score in 2008 was 1.102; in 2010 it was 1.502; in 2012 it was 1.409 and 2013 it was 1.303. This is way below the national average of 3.155 over the same period. Traditional mode of instruction had been the only method of teaching these learners. There was therefore, need to device ways to enable them to participate in learning with ease. Computer Based Learning (CBL) was reported to be effective in the teaching and learning of complex concepts in physics and accounting and could provide a solution in the teaching of mathematics among the learners with physical disabilities. However, attempted use of CBL by these category of learners have not fully succeded despite the Governments effort to ensure all learners irrespective of various disabilities become technologically relevant in line with vision 2030. The purpose of this study was to examine challenges faced by learners with PH in learning Mathematics using CBL methods in Kenya. The conceptual framework was adopted from Winnie and Butter, (1994) model. Saturated sampling was used to get 128 form three students and purposive sampling to get the 5 mathematics teachers from Joyland secondary school for the physically handicapped in Kisumu County, Joytown Secondary School for the physically handicapped in Thika County and Mombasa Secondary school for the physically handicapped in Mombasa county. The instruments used were Computer Assisted Statistics Text (CAST), Student Interview Guide (SIG) and Teacher Interview Guide (TIG). Validity of instruments was established by experts in special needs education. Reliability of instruments was established by test re-test method whereby coefficient of 0.70 and above at p value of 0.05 was considered reliable. The study found significant difference in final exam scores of students receiving traditional instruction and those receiving CBL. There is positive effect of CBL Methods on motivation (r= .561), p<.05) of Secondary school students on learning Mathematics. Professional developmental should be provided to help teachers understand the needs of physical handicapped. Teachers must be committed to continually improving their instructional practice in order to provide a high-quality education for all students, no matter what method of instruction is being used. The findings showed that use of CBL improves the learners’ motivation and achievement in their performance of mathematics.